Gene/Protein Disease Symptom Drug Enzyme Compound
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Query: UMLS:C0344329 (collapse)
 28,634 document(s) hit in 31,850,051 MEDLINE articles (0.00 seconds)

Counterions are critical to the self-assembly of RNA tertiary structure because they neutralize the large electrostatic forces which oppose the folding process. Changes in the size and shape of the Azoarcus group I ribozyme as a function of Mg(2+) and Na(+) concentration were followed by small angle neutron scattering. In low salt buffer, the RNA was expanded, with an average radius of gyration (R(g)) of 53 +/- 1 A. A highly cooperative transition to a compact form (R(g) = 31.5 +/- 0.5 A) was observed between 1.6 and 1.7 mM MgCl(2). The collapse transition, which is unusually sharp in Mg(2+), has the characteristics of a first-order phase transition. Partial digestion with ribonuclease T1 under identical conditions showed that this transition correlated with the assembly of double helices in the ribozyme core. Fivefold higher Mg(2+) concentrations were required for self-splicing, indicating that compaction occurs before native tertiary interactions are fully stabilized. No further decrease in R(g) was observed between 1.7 and 20 mM MgCl(2), indicating that the intermediates have the same dimensions as the native ribozyme, within the uncertainty of the data (+/-1 A). A more gradual transition to a final R(g) of approximately 33.5 A was observed between 0.45 and 2 M NaCl. This confirms the expectation that monovalent ions not only are less efficient in charge neutralization but also contract the RNA less efficiently than multivalent ions.
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PMID:Compaction of a bacterial group I ribozyme coincides with the assembly of core helices. 1476 52

Large RNAs collapse into compact intermediates in the presence of counterions before folding to the native state. We previously found that collapse of a bacterial group I ribozyme correlates with the formation of helices within the ribozyme core, but occurs at Mg2+ concentrations too low to support stable tertiary structure and catalytic activity. Here, using small-angle X-ray scattering, we show that Mg2+-induced collapse is a cooperative folding transition that can be fit by a two-state model. The Mg2+ dependence of collapse is similar to the Mg2+ dependence of helix assembly measured by partial ribonuclease T1 digestion and of an unfolding transition measured by UV hypochromicity. The correspondence between multiple probes of RNA structure further supports a two-state model. A mutation that disrupts tertiary contacts between the L9 tetraloop and its helical receptor destabilized the compact state by 0.8 kcal/mol, while mutations in the central triplex were less destabilizing. These results show that native tertiary interactions stabilize the compact folding intermediates under conditions in which the RNA backbone remains accessible to solvent.
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PMID:RNA tertiary interactions mediate native collapse of a bacterial group I ribozyme. 1621 67